The neurocristopathies encompass a spectrum of developmental disorders characterized by abnormalities of neural crest-derived structures. Neural crest cells are pluripotent progenitors and the mechanisms by which specific cell-fate decisions are regulated have emerged as an important field of study. Many neurocristopathies are characterized by defects in melanocyte differentiation that can result in pigmentation abnormalities and deafness. One example is Waardenburg syndrome that can be caused by mutations in the PAX3, SOX10 or MITF genes. Other neural crest-related disorders are associated with enteric ganglia defects, such as those caused by mutations in the SOX10 or c-RET genes. The Pax3 and Sox10 transcription factors can directly regulate both MITF and c-RET. Here, we show that Pax3 and Sox10 can physically interact and we map the interaction domains. We show that this interaction contributes to Pax3 and Sox10 synergistic activation of a conserved c-RET enhancer and it explains why Sox10 mutants that cannot bind to DNA retain the ability to activate this enhancer in the presence of Pax3. However, in the context of the MITF gene, Pax3 and Sox10 must each bind independently to DNA in order to achieve synergy. This difference is consistent with the different structures of the c-RET and MITF enhancers, and the different mechanisms by which Pax3 binds to these enhancers. These observations explain the phenotype in the mild form of Yemenite deaf-blind syndrome caused by specific SOX10 mutations in the HMG box that abrogate DNA binding without disrupting association with Pax3.